Francesco Vetrini, Lisa C. A. D’Alessandro, Zeynep C

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Bi-allelic Mutations in PKD1L1 Are Associated with Laterality Defects in Humans Francesco Vetrini, Lisa C.A. D’Alessandro, Zeynep C. Akdemir, Alicia Braxton, Mahshid S. Azamian, Mohammad K. Eldomery, Kathryn Miller, Chelsea Kois, Virginia Sack, Natasha Shur, Asha Rijhsinghani, Jignesh Chandarana, Yan Ding, Judy Holtzman, Shalini N. Jhangiani, Donna M. Muzny, Richard A. Gibbs, Christine M. Eng, Neil A. Hanchard, Tamar Harel, Jill A. Rosenfeld, John W. Belmont, James R. Lupski, Yaping Yang The American Journal of Human Genetics Volume 99, Issue 4, Pages 886-893 (October 2016) DOI: 10.1016/j.ajhg.2016.07.011 Copyright © 2016 American Society of Human Genetics Terms and Conditions

Figure 1 Segregation of PKD1L1 Mutations with Laterality Defects in Families 1 and 2 (A) NGS reads in Integrative Genomic Viewer (IGV) and Sanger chromatograms show the c.6473+2_6473+3delTG deletion in family 1: proband (II-3, subject 1), affected brother (II-2, subject 2), unaffected sister (II-1), father (I-1), and mother (I-2). The c.6473+2_6473+3delTG deletion is homozygous in the proband and the affected brother and heterozygous in the parents. The mutation is indicated by red arrows. (B) Plain radiograph of the chest and abdomen of the affected brother in family 1 (subject 2) at birth shows situs ambiguous with levocardia and leftward apex (white “C”), left-sided liver (Liv), right-sided stomach (S); R = right, L = left. (C) CT localizer radiograph of the proband in family 2 (subject 3) demonstrates situs inversus totalis with dextrocardia and rightward apex (C), left-sided liver (Liv), right-sided stomach (S), and right-sided spleen (Sp). Median sternotomy wires are seen as well as a subcutaneous pacemaker (P) with intravascular leads terminating in the left-sided right atrium and subpulmonary ventricle; R = right, L = left. (D) NGS reads in IGV and Sanger chromatograms show the c.5072G>C (p.Cys1691Ser) missense change in family 2: proband (II-1, subject 3) and mother (I-2). The c.5072G>C (p.Cys1691Ser) change is homozygous in the proband and heterozygous in the mother. The mutation is indicated by red arrows. (E) Schematic representation of genomic structure of human PKD1L1, where solid blue rectangles indicate exons and the horizontal bars introns. The exons 32 and 42 are colored in solid red and the mutations with their relative position are shown. The American Journal of Human Genetics 2016 99, 886-893DOI: (10.1016/j.ajhg.2016.07.011) Copyright © 2016 American Society of Human Genetics Terms and Conditions

Figure 2 Alignment and Molecular Modeling of the Impact of p.Cys1691Ser Variant on the GPS Motif (A) Schematic representation of the human PKD1L1 structural domains. PKD1L1 has two Ig-like PKD domains, a REJ domain and a GPS motif in the N-terminal extracellular region, an LH2/Plat domain in the first intracellular loop, and a coiled-coil domain at the C-terminal (CC). (B and C) 3D models of the GPS motif in PDK1L1 in the wild-type (B) and p.Cys1691Ser mutant (C) by Phyre2 based on the GPS motif in the GAIN and HormR domains of human brain angiogenesis inhibitor 3 (BAI3). The five β strands are shown with numbered amino acids corresponding to the coding sequence of PKD1L1. Cys to Ser substitution at the position 1691 (magnification boxed in red) eliminates the highly conserved disulfide bridge between cysteine residues 1691 and 1717 represented by the yellow solid bar. The conserved Leu1722 residue at the putative cleavage site is boxed in blue. (D) Alignment of the GPS motif in PKD1L1, other members of PC-1 family, and G protein couple receptors (GPCRs). The GPS motif contains four conserved cysteines arranged in a specific fashion (C-x2-W-x6-16- W-x4-C-x-10-22-C-x-C) just before the first transmembrane domain. The conserved cysteine (C) residues are boxed; the conserved tryptophan (W) residues are highlighted in magenta. The first cysteine residues are numbered with respect to the protein sequence. PKD1L1 and PKD1 do not have the second and fourth (II and IV) cysteine residues in the conserved positions. The putative cleavage site leucine residues that are located in the turn between the last two β strands of the GPS motif are highlighted in green in the alignment. Highlighted in cyan is the mutant site of PKD1L1 GPS in subject 3 (II-1 from family 2) of this study. Highlighted in red are the previously reported mutant sites in the GPS motif in hPKD1, hBAI3, and hGPR56 and cLAT-1. Abbreviations are as follows: h, human; r, rat; m, mouse; c, C. elegans. (E) ClustalW multiple alignment analysis shows high level evolutionary conservation of the human Cys1691 residue in PKD1L1 across multiple species (highlighted in gray). The American Journal of Human Genetics 2016 99, 886-893DOI: (10.1016/j.ajhg.2016.07.011) Copyright © 2016 American Society of Human Genetics Terms and Conditions